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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Interaction pattern similarity measured by Grim
You can zoom onto the graph by using the mouse to make a selection

Binding Modes are compared using Grim.
For more information, please see the following publication: Desaphy J. et al. Encoding Protein-Ligand Interaction Patterns in Fingerprints and Graphs J. Chem. Inf. Model., 2013, 53 (3), pp 623-637
Binding modes are considered as similar when the similarity value is greater than 0.65


Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
1im2 ADP ATP-dependent protease ATPase subunit HslU

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1im2 ADPATP-dependent protease ATPase subunit HslU / 0.963
1g41 ADPATP-dependent protease ATPase subunit HslU / 0.805
1ht2 ADPATP-dependent protease ATPase subunit HslU / 0.743
1um8 ADPATP-dependent Clp protease ATP-binding subunit ClpX / 0.728
5fl3 ADPPili retraction protein PilT / 0.713
1fnn ADPORC1-type DNA replication protein / 0.711
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.707
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.706
2fna ADPUncharacterized protein / 0.704
3d8b ADPFidgetin-like protein 1 3.6.4 0.703
2gm1 ADPKinesin-like protein KIF11 / 0.702
2c96 ATPPsp operon transcriptional activator / 0.700
3k1j ADPATP-dependent protease Lon / 0.699
3c41 ANPAmino acid ABC transporter / 0.698
3hu1 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.697
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.695
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.694
1w5t ANPORC1-type DNA replication protein 2 / 0.693
4ike ADPAdenylate kinase / 0.693
4jld ADPAdenylate kinase / 0.693
1ofh ADPATP-dependent protease ATPase subunit HslU / 0.692
4gp6 ADPMetallophosphoesterase / 0.692
1z0a GDPRas-related protein Rab-2A / 0.691
2q2z ADPKinesin-like protein KIF11 / 0.689
1mma ADPMyosin-2 heavy chain / 0.686
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.686
4pfp ADPUnconventional myosin-VI / 0.686
4qos ADPPsp operon transcriptional activator / 0.686
1l8q ADPChromosomal replication initiator protein DnaA / 0.685
4d81 ADPAAA ATPase, central domain protein / 0.685
3hu3 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.683
3uk6 ADPRuvB-like 2 3.6.4.12 0.683
1xmv ADPProtein RecA / 0.682
3b1x GNPFerrous iron transport protein B / 0.682
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.681
4qnr ATPPsp operon transcriptional activator / 0.681
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.679
1x1r GDPRas-related protein M-Ras / 0.678
2dft ADPShikimate kinase 2.7.1.71 0.678
2pg2 ADPKinesin-like protein KIF11 / 0.678
4epw GDPGTPase KRas / 0.677
4ww4 ADPRuvB-like helicase / 0.677
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.676
1z2a GDPRas-related protein Rab-23 / 0.676
2dpx GDPGTP-binding protein RAD / 0.676
4jky ADPAdenylate kinase / 0.676
5fv0 ONAESX secretion system protein EccC / 0.676
1ank ANPAdenylate kinase / 0.675
2q2y ADPKinesin-like protein KIF11 / 0.675
4jl6 ADPAdenylate kinase / 0.675
4qbg AP5Adenylate kinase / 0.675
2y65 ADPKinesin heavy chain / 0.674
3ews ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.674
1cxz GSPTransforming protein RhoA / 0.673
4g0n GNPGTPase HRas / 0.673
2uyi ADPKinesin-like protein KIF11 / 0.672
5cyo GDPSeptin-9 / 0.672
2c9o ADPRuvB-like 1 3.6.4.12 0.671
4jl5 ADPAdenylate kinase / 0.671
4ww0 ADPATP-dependent zinc metalloprotease FtsH / 0.671
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.670
1sq5 ADPPantothenate kinase 2.7.1.33 0.670
4asu ADPATP synthase subunit alpha, mitochondrial / 0.670
4dsu GDPGTPase KRas / 0.670
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.670
2vos ADPFolylpolyglutamate synthase / 0.669
4o25 GTPGTP-binding protein Rheb / 0.669
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.669
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.668
1g16 GDPRas-related protein SEC4 / 0.668
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.668
1ii6 ADPKinesin-like protein KIF11 / 0.668
1xts GTPGTP-binding protein Rheb / 0.668
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.668
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.668
1jx2 ADPMyosin-2 heavy chain / 0.667
2axn ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 / 0.667
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.667
2ql6 ADPNicotinamide riboside kinase 1 / 0.667
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.667
3tgp GNPGTPase HRas / 0.667
4jsy GTPMetallophosphoesterase / 0.667
4obe GDPGTPase KRas / 0.667
4q02 GDPGTPase KRas / 0.666
1dvr ATFAdenylate kinase / 0.665
1fmw ATPMyosin-2 heavy chain / 0.665
3tlx ADPAdenylate kinase 2 / 0.665
4epx GDPGTPase KRas / 0.665
4lhv GDPRas-related protein Rab-8A / 0.665
2c9c ATPPsp operon transcriptional activator / 0.664
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.664
2r9v ATPATP synthase subunit alpha / 0.664
3kud GDPGTPase HRas / 0.664
4l8g GDPGTPase KRas / 0.664
1b7t ADPMyosin heavy chain, striated muscle / 0.663
1mab ATPATP synthase subunit alpha, mitochondrial / 0.663
1yra GDPGPN-loop GTPase PAB0955 / 0.663
1zio AP5Adenylate kinase / 0.663
2bbw GP5Adenylate kinase 4, mitochondrial / 0.663
2ce2 GDPGTPase HRas / 0.663
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.663
3kkq GDPRas-related protein M-Ras / 0.663
3mjh GTPRas-related protein Rab-5A / 0.663
4l9s GDPGTPase HRas / 0.663
2j7p GNPSignal recognition particle protein / 0.662
2j7p GNPSignal recognition particle receptor FtsY / 0.662
4cym GCPRas-related protein Rab-32 / 0.662
4dxa GSPRas-related protein Rap-1b / 0.662
4hse ADPChaperone protein ClpB / 0.662
4itr GDPCell division control protein 42 homolog / 0.662
5aun ADPIron-sulfur cluster carrier protein / 0.662
3a58 GNPGTP-binding protein RHO1 / 0.661
4lv6 GDPGTPase KRas / 0.661
4ql3 GDPGTPase KRas / 0.661
4xvq GNPGTPase HRas / 0.661
2rgx AP5Adenylate kinase / 0.660
2zr9 DTPProtein RecA / 0.660
3r9i ADPSeptum site-determining protein MinD / 0.660
1ake AP5Adenylate kinase / 0.659
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.659
1njf ADPDNA polymerase III subunit tau 2.7.7.7 0.659
1ow3 GDPTransforming protein RhoA / 0.659
2ce7 ADPATP-dependent zinc metalloprotease FtsH / 0.659
4l16 ADPFidgetin-like protein 1 3.6.4 0.659
4wa7 GDPGTPase KRas / 0.659
2bc9 GNPGuanylate-binding protein 1 / 0.658
4dzz ADPPlasmid partitioning protein ParF / 0.658
1oix GDPRas-related protein Rab-11A / 0.657
1z0d GDPRas-related protein Rab-5C / 0.657
3t1t GDPProbable gliding protein mglA / 0.657
4dso GSPGTPase KRas / 0.657
4xvr GNPGTPase HRas / 0.657
4ymu ATPABC-type polar amino acid transport system, ATPase component / 0.657
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.656
4pjk ADPMyosin-2 heavy chain / 0.656
3cf0 ADPTransitional endoplasmic reticulum ATPase 3.6.4.6 0.655
4dvg GSPRho family GTPase / 0.655
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.654
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.654
1j7k ATPHolliday junction ATP-dependent DNA helicase RuvB / 0.654
1sxj AGSReplication factor C subunit 1 / 0.654
3k9l GNPGTPase HRas / 0.654
3pfi ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.654
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.653
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.653
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.653
3l8y GNPGTPase HRas / 0.653
3l9h ADPKinesin-like protein KIF11 / 0.653
3rsl GNPGTPase HRas / 0.653
1e94 ANPATP-dependent protease ATPase subunit HslU / 0.652
1ibr GNPGTP-binding nuclear protein Ran / 0.652
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.652
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.652
2d4h 5GPGuanylate-binding protein 1 / 0.652
4jlo ADPAdenylate kinase / 0.652
4ldj GDPGTPase KRas / 0.652
4nh0 ATPESX secretion system protein EccC / 0.652
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.652
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.651
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.651
2bme GNPRas-related protein Rab-4A / 0.651
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.651
3lbi GNPGTPase HRas / 0.651
3oiv GNPGTPase HRas / 0.651
3x1w GDPRas-related protein Rap-1b / 0.651
4l9w GNPGTPase HRas / 0.651
5ftc ADPTPR domain protein / 0.651
1d5c GDPGTPase (Rab6) / 0.650
3q9l ATPSeptum site-determining protein MinD / 0.650
4ma4 ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.650